Hi, I have succeeded to build recent version. Now I have compiled class located at
'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class' How can I run that to generate credential token? I tried 'java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest', but it says ############################################################################################# [heechae@biobrainpool test-classes]$ java org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/airavata/common/exception/ApplicationSettingsException at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) at java.lang.Class.privateGetMethodRecursive(Class.java:3048) at java.lang.Class.getMethod0(Class.java:3018) at java.lang.Class.getMethod(Class.java:1784) at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) Caused by: java.lang.ClassNotFoundException: org.apache.airavata.common.exception.ApplicationSettingsException at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 7 more ############################################################################################ it seems it cannot find dependent classes. I manually copied all required classes to same location and tried to run, but at the end I still got ############################################################################################## Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43) at org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50) Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 2 more ############################################################################################## Thanks, Heejoon. On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <[email protected] > wrote: > The build should work fine now. > > On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <[email protected]> > wrote: > >> Unfortunately, the compile fails at certain point, >> >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] BUILD FAILURE >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Total time: 7:41.368s >> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015 >> [INFO] Final Memory: 95M/3073M >> [INFO] >> ------------------------------------------------------------------------ >> [ERROR] Failed to execute goal >> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile >> (default-compile) on project airavata-client-samples: Compilation failure: >> Compilation failure: >> [ERROR] >> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55] >> incompatible types: java.lang.String cannot be converted to >> org.apache.airavata.model.security.AuthzToken >> [ERROR] >> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65] >> incompatible types: java.lang.String cannot be converted to >> org.apache.airavata.model.security.AuthzToken >> [ERROR] >> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81] >> incompatible types: java.lang.String cannot be converted to >> org.apache.airavata.model.security.AuthzToken >> >> Thanks, >> Heejoon. >> >> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <[email protected]> >> wrote: >> >>> Sorry, I found my JAVA_HOME set to different location even I use java >>> 1.8. >>> >>> Now it seems building goes correctly! >>> >>> Thank you! >>> Heejoon. >>> >>> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <[email protected]> >>> wrote: >>> >>>> Yes. I am using java 1.8 >>>> >>>> [heechae@biobrainpool airavata]$ which java >>>> /packages/jdk1.8.0_65/bin/java >>>> >>>> Thanks, >>>> Heejoon. >>>> >>>> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena < >>>> [email protected]> wrote: >>>> >>>>> Hi Heejoon, >>>>> >>>>> I hope you are using java 1.8. >>>>> >>>>> Thanks.. >>>>> Chathuri >>>>> >>>>> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <[email protected]> >>>>> wrote: >>>>> >>>>>> Hi, Supun, >>>>>> >>>>>> Thank you for fixing that. I updated and do mvn clean install. >>>>>> I got some errors like, >>>>>> >>>>>> INFO] BUILD FAILURE >>>>>> [INFO] >>>>>> ------------------------------------------------------------------------ >>>>>> [INFO] Total time: 7.754s >>>>>> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015 >>>>>> [INFO] Final Memory: 36M/1931M >>>>>> [INFO] >>>>>> ------------------------------------------------------------------------ >>>>>> [ERROR] Failed to execute goal >>>>>> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile >>>>>> (default-compile) on project airavata-data-models: Fatal error compiling: >>>>>> invalid target release: 1.8 -> [Help 1] >>>>>> [ERROR] >>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven with >>>>>> the -e switch. >>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug logging. >>>>>> [ERROR] >>>>>> [ERROR] For more information about the errors and possible solutions, >>>>>> please read the following articles: >>>>>> [ERROR] [Help 1] >>>>>> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException >>>>>> [ERROR] >>>>>> [ERROR] After correcting the problems, you can resume the build with >>>>>> the command >>>>>> [ERROR] mvn <goals> -rf :airavata-data-models >>>>>> >>>>>> Thanks, >>>>>> Heejoon. >>>>>> >>>>>> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hi Heejoon, >>>>>>> >>>>>>> There was an issue in the pom files and I fixed it now. Can you >>>>>>> check whether your build is working now >>>>>>> >>>>>>> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> I got following as well, >>>>>>>> >>>>>>>> [INFO] Scanning for projects... >>>>>>>> [ERROR] The build could not read 2 projects -> [Help 1] >>>>>>>> [ERROR] >>>>>>>> [ERROR] The project >>>>>>>> org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT >>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml) >>>>>>>> has 1 error >>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact >>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and >>>>>>>> 'parent.relativePath' >>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2] >>>>>>>> [ERROR] >>>>>>>> [ERROR] The project >>>>>>>> org.apache.airavata:data-manager-core:0.16-SNAPSHOT >>>>>>>> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml) >>>>>>>> has 1 error >>>>>>>> [ERROR] Non-resolvable parent POM: Could not find artifact >>>>>>>> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and >>>>>>>> 'parent.relativePath' >>>>>>>> points at wrong local POM @ line 5, column 13 -> [Help 2] >>>>>>>> [ERROR] >>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven >>>>>>>> with the -e switch. >>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug >>>>>>>> logging. >>>>>>>> [ERROR] >>>>>>>> [ERROR] For more information about the errors and possible >>>>>>>> solutions, please read the following articles: >>>>>>>> [ERROR] [Help 1] >>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException >>>>>>>> [ERROR] [Help 2] >>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Heejoon. >>>>>>>> >>>>>>>> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> Instead of building only credential store module, could you build >>>>>>>>> from airavata source root. Credential store module depends on >>>>>>>>> airavata-server-configuration and other jars. That should resolve >>>>>>>>> your issue.. >>>>>>>>> >>>>>>>>> Thanks. >>>>>>>>> Chathuri >>>>>>>>> >>>>>>>>> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> Hi, Chathuri, >>>>>>>>>> >>>>>>>>>> Thank you for the explanation. >>>>>>>>>> >>>>>>>>>> I cloned the git and tried to compile credential-store with 'mvn >>>>>>>>>> clean install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got >>>>>>>>>> following errors. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ############################################################################################################### >>>>>>>>>> Downloaded: >>>>>>>>>> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar >>>>>>>>>> (571 KB at 2.8 KB/sec) >>>>>>>>>> [INFO] >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> [INFO] BUILD FAILURE >>>>>>>>>> [INFO] >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> [INFO] Total time: 3:53.576s >>>>>>>>>> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015 >>>>>>>>>> [INFO] Final Memory: 11M/1931M >>>>>>>>>> [INFO] >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> [ERROR] Failed to execute goal on project >>>>>>>>>> airavata-credential-store: Could not resolve dependencies for project >>>>>>>>>> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The >>>>>>>>>> following artifacts could not be resolved: >>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT, >>>>>>>>>> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT, >>>>>>>>>> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not >>>>>>>>>> find >>>>>>>>>> artifact >>>>>>>>>> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT >>>>>>>>>> in >>>>>>>>>> apache.snapshots (http://repository.apache.org/snapshots) -> >>>>>>>>>> [Help 1] >>>>>>>>>> [ERROR] >>>>>>>>>> [ERROR] To see the full stack trace of the errors, re-run Maven >>>>>>>>>> with the -e switch. >>>>>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug >>>>>>>>>> logging. >>>>>>>>>> [ERROR] >>>>>>>>>> [ERROR] For more information about the errors and possible >>>>>>>>>> solutions, please read the following articles: >>>>>>>>>> [ERROR] [Help 1] >>>>>>>>>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException >>>>>>>>>> >>>>>>>>>> ############################################################################################################### >>>>>>>>>> >>>>>>>>>> Any suggestion? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Heejoon. >>>>>>>>>> >>>>>>>>>> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Heejoon, >>>>>>>>>>> >>>>>>>>>>> You need to set up a valid credential store token in the >>>>>>>>>>> credential store (experiment-catalog database has tables related to >>>>>>>>>>> credential store). Same credential store token needs to be set in >>>>>>>>>>> gateway >>>>>>>>>>> profiles. This token is used when airavata ssh to resource, input >>>>>>>>>>> staging >>>>>>>>>>> and all the remote connections with the resource. Credential store >>>>>>>>>>> token is >>>>>>>>>>> the identifier for SSH credential object which contains valid SSH >>>>>>>>>>> keys. >>>>>>>>>>> Refer this code >>>>>>>>>>> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java. >>>>>>>>>>> There are API methods to generate SSH keys as well. You can use any >>>>>>>>>>> of the >>>>>>>>>>> two methods. >>>>>>>>>>> >>>>>>>>>>> Thanks.. >>>>>>>>>>> Chathuri >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae < >>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi, Suresh, >>>>>>>>>>>> >>>>>>>>>>>> Thank you for the help. It correctly parses the email. >>>>>>>>>>>> >>>>>>>>>>>> Now I have another error caused by 'credential token' as below, >>>>>>>>>>>> >>>>>>>>>>>> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, >>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId: >>>>>>>>>>>> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- >>>>>>>>>>>> output >>>>>>>>>>>> staging failed, reason: Provided credential store token is not >>>>>>>>>>>> valid. >>>>>>>>>>>> Please provide the correct credential store token >>>>>>>>>>>> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, >>>>>>>>>>>> processId: PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process >>>>>>>>>>>> status >>>>>>>>>>>> changed FAILED -> FAILED >>>>>>>>>>>> [INFO] Publishing status to rabbitmq... >>>>>>>>>>>> [ERROR] GFac Worker throws an exception >>>>>>>>>>>> org.apache.airavata.gfac.core.GFacException: Error while >>>>>>>>>>>> staging output data >>>>>>>>>>>> at >>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478) >>>>>>>>>>>> at >>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393) >>>>>>>>>>>> at >>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172) >>>>>>>>>>>> at >>>>>>>>>>>> org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105) >>>>>>>>>>>> at >>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) >>>>>>>>>>>> at >>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) >>>>>>>>>>>> at java.lang.Thread.run(Thread.java:745) >>>>>>>>>>>> >>>>>>>>>>>> I actually set 'false' for storing credential in the >>>>>>>>>>>> 'airavata-server.properties' file as bellow >>>>>>>>>>>> >>>>>>>>>>>> start.credential.store=false >>>>>>>>>>>> >>>>>>>>>>>> but it seems still they are active. >>>>>>>>>>>> >>>>>>>>>>>> Thank you, >>>>>>>>>>>> Heejoon. >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru < >>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Heejoon, >>>>>>>>>>>>> >>>>>>>>>>>>> You will need to configure your email within gfac-config.yaml >>>>>>>>>>>>> (you will find it in the bin directory). >>>>>>>>>>>>> >>>>>>>>>>>>> If you can add your email to: >>>>>>>>>>>>> >>>>>>>>>>>>> - jobManagerType: SLURM >>>>>>>>>>>>> commandOutputParser: >>>>>>>>>>>>> org.apache.airavata.gfac.impl.job.SlurmOutputParser >>>>>>>>>>>>> emailParser: >>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser >>>>>>>>>>>>> resourceEmailAddresses: >>>>>>>>>>>>> - SDSC Admin <[email protected]> # comet >>>>>>>>>>>>> - [email protected] # stampede >>>>>>>>>>>>> - [email protected] >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Suresh >>>>>>>>>>>>> >>>>>>>>>>>>> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> > >>>>>>>>>>>>> > Hi, Suresh, >>>>>>>>>>>>> > >>>>>>>>>>>>> > I am using one month old version of PGA and Airavata server. >>>>>>>>>>>>> Both were recent version at that time. >>>>>>>>>>>>> > >>>>>>>>>>>>> > apache-airavata-server-0.16-SNAPSHOT >>>>>>>>>>>>> > >>>>>>>>>>>>> > Thank you, >>>>>>>>>>>>> > Heejoon. >>>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> > Hi Heejoon, >>>>>>>>>>>>> > >>>>>>>>>>>>> > Are you using Airavata 0.15 or 0.16 for this purpose? >>>>>>>>>>>>> > >>>>>>>>>>>>> > Suresh >>>>>>>>>>>>> > >>>>>>>>>>>>> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> Hi, >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> I have succeeded run job with SLURM. >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> Now, the job monitoring through email causes some errors as >>>>>>>>>>>>> bellow. >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> It seems the Airavata server correctly log in the email >>>>>>>>>>>>> account and bring email list, but it could not parse it correctly. >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> >>>>>>>>>>>>> ################################################################################# >>>>>>>>>>>>> >> [ERROR] [EJM]: Error parsing email message >>>>>>>>>>>>> =====================================> >>>>>>>>>>>>> >> org.apache.airavata.common.exception.AiravataException: >>>>>>>>>>>>> [EJM]: Couldn't identify Resource job manager type from address >>>>>>>>>>>>> [email protected] >>>>>>>>>>>>> >> at >>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160) >>>>>>>>>>>>> >> at >>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144) >>>>>>>>>>>>> >> at >>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239) >>>>>>>>>>>>> >> at >>>>>>>>>>>>> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208) >>>>>>>>>>>>> >> at java.lang.Thread.run(Thread.java:745) >>>>>>>>>>>>> >> [ERROR] FROM: [email protected] >>>>>>>>>>>>> >> [ERROR] TO: [email protected] >>>>>>>>>>>>> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, >>>>>>>>>>>>> Run time 00:00:01, COMPLETED, ExitCode 0 >>>>>>>>>>>>> >> >>>>>>>>>>>>> ################################################################################# >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> Thank you, >>>>>>>>>>>>> >> Heejoon. >>>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Thank you >>>>>>> Supun Nakandala >>>>>>> Dept. Computer Science and Engineering >>>>>>> University of Moratuwa >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> > > > -- > Thank you > Supun Nakandala > Dept. Computer Science and Engineering > University of Moratuwa >
